[gmx-users] Errors in building GMX 5.1.x on Redhat 6.5 (a lot of "Undefined reference to ..")

[Mark Abraham]

Hi,

These are linking errors that look like they are from not linking the
appropriate version of the C++ standard library. I highly recommend leaving
the system libraries alone on redhat systems, and instead compiling with
the devtoolset packages.

Thanks for the Cygwin report. People often report problems that look like
they come from broken systems, and we rarely hear of a resolution.

Mark

On Fri, 3 Feb 2017 05:55 Qing Lv <lvqingjiejie at 163.com> wrote:

> Hi Colleagues,
>
>
> I am trying to build GMX 5.1.x (tried 5.1.4, 5.1.1, & 5.1) on a Redhat 6.5
> server; I have updated GCC compiler and all dependent libraries (tried GCC
> 4.9.4 and GCC 6.3.0). (The built-in compiler of Redhat 6.5 is GCC 4.4.7,
> which is too old.)
> I used the commmand
> export CC=gcc
> export CXX=gcc
> cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON
>         # No errors reported till now
> make
> When 100% completed, I got a lot of error messages like
> ../../lib/libgromacs.so.1.0.0: Undefined reference to
> ‘std::runtime_error::what() const’
> ../../lib/libgromacs.so.1.0.0: Undefined reference to ........
> ../../lib/libgromacs.so.1.0.0: Undefined reference to ........
> And the error messages finished with
> collect2: Error: ld returns 1
> make[2]: *** [bin/template] Error 1
> make[1]: *** [share/template/CMakeFiles/template.dir/all] Error 2
> make: *** [all] Error 2
>
>
> Any friends can help? Thanks
> BTW, I have just successfully compiled GMX 5.1.4 on Cygwin.
>
>
> Qing
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